Re: What goes around comes around

From: Preston Garrison <>
Date: Fri Oct 07 2005 - 22:55:44 EDT

>I'd like to see the "thousands of TE
>insertions" to which you are referring.


I have more quibbles, but they will have to wait for later.


Here's the ref I was thinking of. These guys found over 900
orthologous insertions in a 1.5 Mb alignment of human and chimp. So,
extrapolating we're talking millions, really. The total number in a
set of 9 species that were fully sequenced in this segment contained
over 1000 sites. The total is not much higher for the whole group,
because the more distant species (dog, cat, cow etc) contained only a
few sites in this region. This is the same data that Frances Collins
referred to in his PSCF article. If I remember right there were ~50
anomalous insertions in the nine species set, but I'm not sure. This
is a complicated paper and I haven't studied it carefully yet. I'm
sure you will find much to object to. :)

Genome Res. 2005 Jul;15(7):998-1006.

Orthologous repeats and mammalian phylogenetic inference.
Bashir A, Ye C, Price AL, Bafna V.

Determining phylogenetic relationships between species is a difficult
problem, and many phylogenetic relationships remain unresolved, even
among eutherian mammals. Repetitive elements provide excellent
markers for phylogenetic analysis, because their mode of evolution is
predominantly homoplasy-free and unidirectional. Historically,
phylogenetic studies using repetitive elements have relied on
biological methods such as PCR analysis, and computational inference
is limited to a few isolated repeats. Here, we present a novel
computational method for inferring phylogenetic relationships from
partial sequence data using orthologous repeats. We apply our method
to reconstructing the phylogeny of 28 mammals, using more than 1000
orthologous repeats obtained from sequence data available from the
NISC Comparative Sequencing Program. The resulting phylogeny has
robust bootstrap numbers, and broadly matches results from previous
studies which were obtained using entirely different data and
methods. In addition, we shed light on some of the debatable aspects
of the phylogeny. With rapid expansion of available partial sequence
data, computational analysis of repetitive elements holds great
promise for the future of phylogenetic inference.

But wait! There's more!
Here's a bonus. This is new. I haven't read it yet.

Genome Res. 2005 Sep;15(9):1243-9.

Genomic deletions and precise removal of transposable elements
mediated by short identical DNA segments in primates.

van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL.

Insertion of transposable elements is a major cause of genomic
expansion in eukaryotes. Less is understood, however, about
mechanisms underlying contraction of genomes. In this study, we show
that retroelements can, in rare cases, be precisely deleted from
primate genomes, most likely via recombination between 10- to 20-bp
target site duplications (TSDs) flanking the retroelement. The
deleted loci are indistinguishable from pre-integration sites,
effectively reversing the insertion. Through human-chimpanzee-Rhesus
monkey genomic comparisons, we estimate that 0.5%-1% of apparent
retroelement "insertions" distinguishing humans and chimpanzees
actually represent deletions. Furthermore, we demonstrate that 19% of
genomic deletions of 200-500 bp that have occurred since the
human-chimpanzee divergence are associated with flanking identical
repeats of at least 10 bp. A large number of deletions internal to
Alu elements were also found flanked by homologies. These results
suggest that illegitimate recombination between short direct repeats
has played a significant role in human genome evolution. Moreover,
this study lends perspective to the view that insertions of
retroelements represent unidirectional genetic events.
Received on Fri Oct 7 22:57:06 2005

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